UK Coal said chief executive Jon Lloyd would continue to receive 375,000 in pay, while finance director David Brocksom would get 234,675 after separate accidents in two of the firm's deep mines in 2009.
The pair's bonuses were also cut, reflecting missed targets on safety, cash flow, profit and group coal sales.
Consequently, Lloyd and Brocksom's reward payments were reduced by 20 per cent and 14 per cent respectively to 36,000 and 21,120.
UK Coal also posted a pre-tax loss of 129.1 million for the year to December 2009, compared with a 15.6m deficit in 2008.
Chairman David Jones said the year had been "extremely challenging" for the group as financial results were "substantially affected by geological issues" in each of its deep mines.
The mining division slipped from a combined operating loss of 2.4m in 2008 to a deficit of 68.6m last year.
In July, a worker at its Thoresby site died when pipes being unloaded underground slipped from the transport vehicle.
This accident was followed by a fatality at the Kellingley mine, resulting in the Health and Safety Executive (HSE) banning the firm from continuing to operate on the affected face until it had replaced components in its roof supports.
Even when the panel was reopened, it did not return to its previous levels of output and the firm is now concentrating its attention on a new face.
The two fatal injuries at UK Coal last year compare with one in 2008, and there were 27 major injury accidents reported to the HSE, from 26 a year earlier.
"The directors deeply regret the fatal accidents at Thoresby colliery and Kellingley colliery involving experienced underground workmen in July and October 2009" the firm said.
UK Coal last year appointed a safety director, who reports to the chief executive.
Production for last year was seven million tonnes, from 7.9m tonnes in 2008 and the firm now expects to produce about 6m tonnes from deep mines and a further 1.6m from surface mines this year.
It said while problems had persisted into the first quarter of 2010, these had now been addressed.
The group said its property division, which suffered in the recession-hit market last year, was performing in line with expectations.